Report Bug - BioGearshttps://biogearsengine.com/forums/categories/report-a-bug/feed.rss
Fri, 22 Feb 2019 14:14:11 +0000Report Bug - BioGearsen-CARPi, "Could not find all dependent libraries"https://biogearsengine.com/forums/discussion/78/rpi-could-not-find-all-dependent-libraries
Thu, 01 Feb 2018 23:22:41 +0000MEwer78@/forums/discussionsInstallation went fine. The very first thing I did once the system started was download the RPi versions of BioGears Toolkit and SDK. I extracted the toolkit into ~/Downloads/toolkit, and ran ./BioGearsGUI.sh, but it failed with the following logs (omitting parts of the stack traces, because of character limit):

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pi@raspberrypi:~/Downloads/toolkit $ ./BioGearsGUI.sh INFO FileUtils::69::Loading native library : /home/pi/Downloads/toolkit/release/xerces-c_3_1_vc120ERROR FileUtils::91::Unable to load /home/pi/Downloads/toolkit/release/xerces-c_3_1_vc120java.lang.UnsatisfiedLinkError: no xerces-c_3_1_vc120 in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at mil.tatrc.physiology.utilities.FileUtils.loadLibrary(FileUtils.java:86)... at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)INFO FileUtils::69::Loading native library : /home/pi/Downloads/toolkit/release/libxerces-c-3-1ERROR FileUtils::91::Unable to load /home/pi/Downloads/toolkit/release/libxerces-c-3-1java.lang.UnsatisfiedLinkError: no libxerces-c-3-1 in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at mil.tatrc.physiology.utilities.FileUtils.loadLibrary(FileUtils.java:86)... at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)INFO FileUtils::69::Loading native library : /home/pi/Downloads/toolkit/release/libxerces-c-3.1INFO FileUtils::69::Loading native library : /home/pi/Downloads/toolkit/release/log4cppERROR FileUtils::91::Unable to load /home/pi/Downloads/toolkit/release/log4cppjava.lang.UnsatisfiedLinkError: no log4cpp in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at mil.tatrc.physiology.utilities.FileUtils.loadLibrary(FileUtils.java:86)... at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)INFO FileUtils::69::Loading native library : /home/pi/Downloads/toolkit/release/DataModelBindingsERROR FileUtils::91::Unable to load /home/pi/Downloads/toolkit/release/DataModelBindingsjava.lang.UnsatisfiedLinkError: no DataModelBindings in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at mil.tatrc.physiology.utilities.FileUtils.loadLibrary(FileUtils.java:86)... at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)INFO FileUtils::69::Loading native library : /home/pi/Downloads/toolkit/release/CommonDataModelERROR FileUtils::91::Unable to load /home/pi/Downloads/toolkit/release/CommonDataModeljava.lang.UnsatisfiedLinkError: no CommonDataModel in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at mil.tatrc.physiology.utilities.FileUtils.loadLibrary(FileUtils.java:86)... at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)INFO FileUtils::69::Loading native library : /home/pi/Downloads/toolkit/release/CommonDataModelTestERROR FileUtils::91::Unable to load /home/pi/Downloads/toolkit/release/CommonDataModelTestjava.lang.UnsatisfiedLinkError: no CommonDataModelTest in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at mil.tatrc.physiology.utilities.FileUtils.loadLibrary(FileUtils.java:86)... at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)INFO FileUtils::69::Loading native library : /home/pi/Downloads/toolkit/release/CommonDataModelJNIERROR FileUtils::91::Unable to load /home/pi/Downloads/toolkit/release/CommonDataModelJNIjava.lang.UnsatisfiedLinkError: no CommonDataModelJNI in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) at java.lang.Runtime.loadLibrary0(Runtime.java:870) at java.lang.System.loadLibrary(System.java:1122) at mil.tatrc.physiology.utilities.FileUtils.loadLibrary(FileUtils.java:86)... at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)Exception in thread "AWT-EventQueue-0" java.lang.ExceptionInInitializerError at mil.tatrc.physiology.datamodel.properties.CommonUnits$LengthUnit.validUnit(CommonUnits.java:848) at mil.tatrc.physiology.datamodel.properties.SEScalarLength.validUnit(SEScalarLength.java:96) at mil.tatrc.physiology.datamodel.properties.SEScalar.setValue(SEScalar.java:273) at mil.tatrc.physiology.datamodel.properties.SEScalar.load(SEScalar.java:77) at mil.tatrc.physiology.datamodel.patient.SEPatient.load(SEPatient.java:139) at mil.tatrc.physiology.datamodel.patient.SEPatient.loadPatientFile(SEPatient.java:265) at mil.tatrc.physiology.biogears.gui.scenario.ScenarioEditor.(ScenarioEditor.java:257) at mil.tatrc.physiology.biogears.gui.GUIContext.(GUIContext.java:56) at mil.tatrc.physiology.biogears.gui.GUIContext.getAppFrame(GUIContext.java:72) at mil.tatrc.physiology.biogears.gui.BioGearsGUI.createAndShowUI(BioGearsGUI.java:29) at mil.tatrc.physiology.biogears.gui.BioGearsGUI$1.run(BioGearsGUI.java:22) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)Caused by: java.lang.RuntimeException: Could not find all dependent libraries : [log4cpp, DataModelBindings, CommonDataModel, CommonDataModelTest, CommonDataModelJNI] at mil.tatrc.physiology.utilities.UnitConverter.(UnitConverter.java:52) ... 25 more

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Some of those libraries look internal to BioGears, rather than things to install. I can't find a README or INSTALLATION file. If there were extra steps to get this working on a clean RPi, I'd have expected there to be mention of it on the site or at least in a README. I had the same problem earlier with an older RPi Zero W, but assumed it was because the OS was outdated or something. Any idea what's up?

Thanks!]]>Error in Morphine substancehttps://biogearsengine.com/forums/discussion/72/error-in-morphine-substance
Fri, 01 Dec 2017 16:10:57 +0000NurNur72@/forums/discussionsAt first, sorry for my english, it's not very good and I hope that You understand me.I have the next trouble with morphine infusion in toolkit. When I use this substance in SubstanceBolus and in SubstanceInfusion I have the next error:

ERROR : : [0(s)] Value is NaN

If I use scenarios (for example Scenarios\Drug\Morphine.xml, Scenarios\Drug\MorphineOverdose.xml) whit morphine i have the next error:

]]>Hemorrhage action not functional in BioGears V6.2 GUIhttps://biogearsengine.com/forums/discussion/74/hemorrhage-action-not-functional-in-biogears-v6-2-gui
Wed, 13 Dec 2017 16:03:08 +0000barnesj74@/forums/discussionsIf "okay" is click "Action is not valid" appears. I must cancel out of the box.

The other Actions work properly and this was not an issue on previous BioGears version.

I have not tried to use the hemorrhage action by writing an XML file rather than using the GUI to do this.]]>Error when I run build-linux.sh in the new release 6.2.0https://biogearsengine.com/forums/discussion/68/error-when-i-run-build-linux-sh-in-the-new-release-6-2-0
Mon, 02 Oct 2017 04:33:58 +0000mousalgf68@/forums/discussionsI get the following error when I try compile any example scenario in src folder using build-linux.sh.I never got it in the previous version.

Thanks,Farooq]]>unable to load saved scenarios if output data request output is presenthttps://biogearsengine.com/forums/discussion/42/unable-to-load-saved-scenarios-if-output-data-request-output-is-present
Wed, 02 Aug 2017 19:42:56 +0000barnesj42@/forums/discussionsCMake issue in clean environmenthttps://biogearsengine.com/forums/discussion/41/cmake-issue-in-clean-environment
Tue, 01 Aug 2017 17:48:18 +0000hscheirich41@/forums/discussions"env variable has not been specified. Make sure when calling cmake a valid environment is specified via -Denv=". Looking at the source it seems that there is a default value being assigned "msvc" this default value does not work (besides that this will be the wrong default under some of the other environments).

In line 5 the variable is created SET(env "" CACHE STRING ""), The set in line 8 in the makefile uses the following form SET(env "msvc" CACHE STRING "") per cmake docs https://cmake.org/cmake/help/v3.0/command/set.html SET with CACHE will create a new variable but not update it. This means that the default value will never be assigned and the empty value from line 5 persists through the following block.

Error:No Build errors. All the projects are built successfully.During run-time, it throws the following error in BioGearsScenarioDriver.exe console "Could not open ./UCEDefs.txt"In the output window, I can see "xerces-c_3_1_vc120.dll-Cannot find or open the PDB file"

Troubleshooting: The debug folder ,that is created after running cmake in Ant, does not contain the xerces dll. This Dll file is missing in the bin/debug folder.

I manually placed the dll file(that was there in previous version) in the debug folder and built the solution again. No luck. The same error appeared and I noticed that the dll was not accessed at all. The dll file is unblocked and it has full access.

Also, would like to know which project should be the start-up project while executing the solution. I tried with BioGearsScenarioDriver and UnitTestDriver as my start-up projects individually(since only those two projects had .exe files).

Am I missing any step? Is there any code level change to be done? ]]>Trouble with the Toolkit GUIhttps://biogearsengine.com/forums/discussion/3/trouble-with-the-toolkit-gui
Fri, 07 Nov 2014 21:14:21 +0000mghackett3@/forums/discussionsI'm trying to use the toolkit to run some of the provided scenarios to get a feel for things. I can run scenarios from the command line without issues (get results, graphs, etc..). When I use the GUI, I can load the scenario, choose my desired outputs, but when I execute, the graphs are all blank. It seems like nothing is actually being executed. Any idea whats going on? Also, I've tried to load some scenarios (like CombatMultiTrauma) and it says its not a valid scenario file. Is the GUI just having issues? ]]>Norton reported threat "Suspicious.Cloud.7.EP" in dllhttps://biogearsengine.com/forums/discussion/13/norton-reported-threat-suspicious-cloud-7-ep-in-dll
Mon, 30 Mar 2015 22:37:07 +0000acorbett13@/forums/discussionsHere are some details: